LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-605-g5eb61491f0-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread.
  using 1 OpenMP thread(s) per MPI task
# May 2025
# Test script for MD-KMC accelerated diffusion testing in LAMMPS
# Created by Jacob Tavenner, Baylor University

# Initiation -------------------------------------
units           metal
dimension       3
boundary        p p p
atom_style      atomic

# Atom Definition --------------------------------
lattice fcc 3.762
Lattice spacing in x,y,z = 3.762 3.762 3.762
region          whole block 0 1 0 1 0 1
create_box      2 whole
Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
  1 by 2 by 2 MPI processor grid
create_atoms    1 region whole
Created 4 atoms
  using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
  create_atoms CPU = 0.000 seconds

replicate 6 16 6
Replication is creating a 6x16x6 = 576 times larger system...
  orthogonal box = (0 0 0) to (22.572 60.192 22.572)
  1 by 4 by 1 MPI processor grid
  2304 atoms
  replicate CPU = 0.000 seconds

region      puck block INF INF 7 9 INF INF
set         region puck type 2
Setting atom values ...
  360 settings made for type

# Force Fields -----------------------------------
pair_style      meam
pair_coeff      * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08

# Settings ---------------------------------------
timestep        0.002
thermo          100

# Computations -----------------------------------
compute         voroN all voronoi/atom neighbors yes

run             0
WARNING: No fixes with time integration, atoms won't move
For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 6.8
  ghost atom cutoff = 6.8
  binsize = 3.4, bins = 7 18 7
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair meam, perpetual
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
  (2) pair meam, perpetual, half/full from (1)
      attributes: half, newton on
      pair build: halffull/newton
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0             -9674.3728      0             -9674.3728     -212400.94    
Loop time of 4.3735e-06 on 4 procs for 0 steps with 2304 atoms

0.0% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0          | 0          | 0          |   0.0 |  0.00
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0          | 0          | 0          |   0.0 |  0.00
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 4.374e-06  |            |       |100.00

Nlocal:            576 ave         576 max         576 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:           2131 ave        2131 max        2131 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:          24768 ave       24768 max       24768 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs:        49536 ave       49536 max       49536 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 198144
Ave neighs/atom = 86
Neighbor list builds = 0
Dangerous builds = 0
thermo_style    custom step temp press pxx pyy pzz lx ly lz vol pe

# Execution --------------------------------------

velocity    all create 2400 908124 loop geom
fix         temp all npt temp 1000 1000 1000 aniso 0 0 1
fix         mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
thermo_style    custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
#dump           dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym

run 1000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- fix neighbor/swap command: doi:10.1016/j.commatsci.2022.111929

@Article{Tavenner2023111929,
 author = {Jacob P. Tavenner and Mikhail I. Mendelev and John W. Lawson},
 title = {Molecular dynamics based kinetic Monte Carlo simulation for accelerated diffusion},
 journal = {Computational Materials Science},
 year = {2023},
 volume = {218},
 pages = {111929}
 url = {https://dx.doi.org/10.1016/j.commatsci.2022.111929}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
   Step          Temp          Press           Pxx            Pyy            Pzz             Lx             Ly             Lz           Volume         PotEng        f_mc[1]        f_mc[2]    
         0   2400          -187517.52     -187464.28     -188202.86     -186885.42      22.572         60.192         22.572         30667.534     -9674.3728      0              0            
       100   1688.7809      13746.894      14218.282      14190.983      12831.417      21.636615      57.726346      21.637269      27025.008     -9601.4799      24             24           
       200   1585.0272     -6497.2882     -7280.7893     -5297.3951     -6913.6802      21.716781      58.142867      21.714094      27417.864     -9571.8204      48             45           
       300   1592.737       1747.6515      2738.4114      1924.1359      580.40727      21.676942      58.130592      21.647155      27277.439     -9574.5368      72             68           
       400   1594.154       852.39952     -369.56275      1867.5224      1059.2389      21.659314      58.220677      21.640495      27289.096     -9574.1977      96             89           
       500   1616.8485     -1466.6184     -1965.5854     -2117.4507     -316.81912      21.622512      58.328889      21.660903      27319.101     -9580.0369      120            112          
       600   1560.0956      1162.0193      2410.2796     -925.45844      2001.2369      21.637185      58.168753      21.700261      27312.124     -9564.0088      144            136          
       700   1583.4354      1031.9177      243.6789       5034.5413     -2182.467       21.682521      57.96166       21.718651      27295.022     -9570.2301      168            158          
       800   1618.7711     -2148.2603     -4066.0779     -863.23022     -1515.4726      21.694024      58.144275      21.659535      27320.975     -9581.5884      192            181          
       900   1598.9132     -764.84277      413.68636     -2395.8324     -312.3823       21.650745      58.249779      21.651506      27305.821     -9575.9563      216            204          
      1000   1603.2739      240.94022      606.79481      644.45464     -528.42878      21.661235      58.138319      21.674995      27296.357     -9577.7462      240            228          
Loop time of 8.90243 on 4 procs for 1000 steps with 2304 atoms

Performance: 19.410 ns/day, 1.236 hours/ns, 112.329 timesteps/s, 258.806 katom-step/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 7.5993     | 7.7187     | 7.8278     |   3.8 | 86.70
Neigh   | 0.056181   | 0.059129   | 0.062043   |   1.1 |  0.66
Comm    | 0.052658   | 0.14746    | 0.25458    |  24.3 |  1.66
Output  | 0.00018588 | 0.00019825 | 0.00023195 |   0.0 |  0.00
Modify  | 0.95669    | 0.97388    | 0.99047    |   1.6 | 10.94
Other   |            | 0.00311    |            |       |  0.03

Nlocal:            576 ave         619 max         531 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost:        2159.25 ave        2181 max        2126 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Neighs:        32404.8 ave       36204 max       28467 min
Histogram: 1 0 1 0 0 0 0 0 1 1
FullNghs:      64809.5 ave       72517 max       56929 min
Histogram: 1 1 0 0 0 0 0 0 1 1

Total # of neighbors = 259238
Ave neighs/atom = 112.51649
Neighbor list builds = 62
Dangerous builds = 0

#write_data     pulse_center.data
Total wall time: 0:00:08
